Package index • chromatographR

Package overview

chromatographR chromatographR-package: chromatographR

Analysis functions

reexports read_chroms: Read chromatograms.

preprocess(): Preprocess time/wavelength data

correct_rt(): Correct retention time

correct_peaks(): Correct peak positions according to a PTW warping model

get_peaks(): Get peak list.

get_peaktable(): Converts peak list into an ordered peak table.

attach_metadata(): Attach experimental metadata

attach_ref_spectra(): Attach reference spectra

normalize_data(): Normalize peak table or chromatograms

cluster_spectra(): Cluster spectra

Visualization functions

plot_all_spectra(): Plot all spectra for chosen peak.

plot_chroms(): Plot traces from list of chromatograms.

plot_chroms_heatmap(): Plot chromatograms as heatmap

plot_spectrum(): Plot spectrum from peak table

boxplot(<peak_table>): Make boxplot from peak table.

mirror_plot(): Make mirror plot from peak table.

scan_chrom(): Plot spectra by clicking on the chromatogram.

plot(<peak_list>): Plot fitted peak shapes.

plot(<peak_table>): Plot spectrum from peak table

plot(<ptw_list>): Plot PTW alignments

Utility functions

combine_peaks(): Combine peaks

filter_peaks(): Filter peak lists

filter_peaktable(): Filter peak table

merge_peaks(): Merge split peaks

get_times(): Get retention times

get_lambdas(): Get lambdas

reshape_chroms(): Reshape chromatograms

reshape_peaktable(): Reshape peaktable

subset(<peak_table>): Subset peak table

write_peaktable(): Export peak table

Data objects

Sa: Raw goldenrod root chromatograms

Sa_pr: Preprocessed goldenrod root chromatograms

Sa_warp: Warped goldenrod root chromatograms.

pk_tab: Goldenrod peak table